Tissue Transcriptome Research Articles

Renal and Peripheral Blood Transcriptome Signatures That Predict Treatment Response in Proliferative Lupus Nephritis-A Prospective Study.

Mechanisms contributing to non-response to treatment in lupus nephritis (LN) are unclear. We characterised the transcriptome of paired peripheral blood mononuclear cells (PBMCs) and renal tissues in LN before and after cyclophosphamide (CYC) treatment and identified markers that predicted treatment response. Total RNA isolated from paired PBMCs (n = 32) and renal tissues (n = 25) of 16 proliferative LN before CYC treatment, 6 months post-treatment, and during renal flare, was sequenced on Illumina Novaseq-6000 platform. Post-treatment, eight patients were clinical responders (CR), of whom four flared (FL), and eight were non-responders (NR). Comparative transcriptomic analyses before and after treatment within CR, NR, and FL groups was performed using DESeq2. Weighted gene co-expression network analysis (WGCNA) and ROC analysis was performed to identify and validate hub genes predictive of treatment response. Based on this, we observed that pathways such as degradation of cell cycle proteins, expression of G0 and G1 phase proteins, and apoptosis, were upregulated in CR PBMCs post-treatment, while IFN-γ signalling and ECM organisation were downregulated. In NR PBMCs, ECM molecules, neddylation and BCR signalling were upregulated post-CYC treatment, while in NR renal tissue, TLR, IFN and NF-κB signalling pathways were upregulated. In FL PBMCs, neutrophil degranulation and ROS and RNS production in phagocytes were downregulated following treatment, whereas, in the corresponding renal tissue, cell-ECM interactions and ISG15 antiviral mechanism were downregulated. After WGCNA and subsequent ROC analysis, TENM2, NLGN1 and AP005230.1 from PBMCs each predicted NR (AUC-0.91; p = 0.03), while combined model improved prediction (AUC-0.94; p = 0.02). AP005230.1 from renal tissue also predicted non-response (AUC-0.94; p = 0.01) and AC092436.3 from PBMCs predicted renal flare (AUC-0.81; p = 0.04). Our study identified significant DEGs/pathways specific to different treatment outcomes and hub genes that predicted non-response and renal flare.

Adipose tissue transcriptome in patients switching efavirenz or a protease inhibitor to raltegravir compared to people without HIV.

To study the subcutaneous adipose tissue (SAT) transcriptome in people with HIV (PWH) switching efavirenz (EFV) or a protease inhibitor (PI) to raltegravir and to compare the transcriptome of PWH to those of people without HIV (PWoH). PWH (n = 36) on EFV (n = 22) or a PI (n = 14) based ART regimen were randomized to switch to RAL (n = 15) or to continue unchanged medication (n = 17). PWoH (n = 10), comparable in age and body mass index, were included for comparison. SAT gene expression was analyzed via RNA sequencing (Illumina Stranded mRNA library prep). At baseline, only 51 out of 19930 genes showed differential expression (FDR <0.05) between PWH and PWoH. Differentially expressed genes in PWH were identified as being HIV host factors or were associated with immune response, lipid metabolism, adipogenesis, apoptosis regulation, DNA/RNA metabolism, and cell structures. Mitochondria-encoded genes were consistently downregulated in PWH. Intergroup variations among PWH using different ART (EFV, PI, RAL) were not significant, and switching EFV or a PI to RAL did not induce substantial changes in the SAT transcriptome. While some specific genes linked to HIV are differentially expressed in PWH compared to PWoH, the overall SAT transcriptome remains relatively stable across various antiretroviral treatments and upon switching from EFV/PI to RAL. These findings enhance our understanding of the molecular landscape on SAT in the context of HIV and ART.

Fibrinogen Alpha Chain as a Potential Serum Biomarker for Predicting Response to Cisplatin and Gemcitabine Doublet Chemotherapy in Lung Adenocarcinoma: Integrative Transcriptome and Proteome Analyses

Cisplatin combined with gemcitabine, a doublet regimen, is the first-line treatment for patients with advanced lung adenocarcinoma (ADC); however, the treatment response remains poor. This study aimed to identify potential biomarkers for predicting response to cisplatin and gemcitabine. Tissue transcriptome and blood proteome analyses were conducted on 27 patients with lung ADC. Blood-derived proteins that reflected tissue-specific biomarkers were obtained using Venn diagrams. The candidate proteins were validated by Western blotting. Lentivirus-mediated short hairpin RNA interference was used to verify the functional roles of the candidate proteins in human A549 cells. We identified 417 differentially expressed genes, including 52 upregulated and 365 downregulated genes, and 31 differentially expressed proteins, including 26 upregulated and 5 downregulated proteins. Integrative analysis revealed the presence of alpha-1-acid glycoprotein 1 (A1AG1) and fibrinogen alpha chain (FGA or FIBA) in both the tissue and serum. FGA levels were elevated in responders compared to non-responders, and reduced serum FGA levels were correlated with resistance to this regimen. Moreover, FGA knockdown in A549 cells resulted in resistance to the doublet regimen. Our findings indicate that FGA is a tissue-specific serum protein that may function as a blood-based biomarker to predict the response of patients with lung ADC to cisplatin plus gemcitabine chemotherapy.

Combining resistance indicators, metabolomes and transcriptomes to reveal correlations in disease and cold resistance in tea plant and analyze the key domain NB-ARC.

Integration of resistance indicators, metabolomes, and transcriptomes to elucidate that there is a positive correlation between disease susceptibility and cold tolerance in tea plants. The flavonoid pathway was found to be the major metabolic and transcriptional enrichment pathway. A key domain NB-ARC was identified through joint analysis, along with analysis of key domains within the NB-ARC protein. Tea is a healthy beverage and the tea plant is a woody plant rich in secondary metabolites. In the face of abnormal climate change year by year, it is important to investigate the mechanisms by which tea plants resist both biotic and abiotic stresses. In this study, we found different tea plant cultivars were evaluated for cold and disease resistance have highly correlated. Subsequently, two cold and fungal resistant cultivars were screened from a Shuixian population that had been cold domesticated for 50years, and transcriptome and metabolome assays were performed on the two materials under cold and anthracnose stresses, using Baiye Dancong as a control. The analyses found that differential metabolites were most enriched in the flavonoid pathway and differentially expressed genes were most enriched in the pathway related to disease course after pathogen stress and cold stress. Combined metabolome and transcriptome analyses identified 30 genes that were positively correlated with flavonoid content after pathogen stress and cold stress, of which the number of genes with NB-ARC structural domains was 11, which accounted for the largest proportion. These 11 genes with NB-ARC structural domains were analyzed by family analysis and found to be highly involved in different tissues transcriptomes of tea plants, indicating the importance of the NB-ARC structural domains in biotic and abiotic stresses, and providing a theoretical basis of analysis for the subsequent related studies. In this study, through the identification of resistance in different varieties of tea plant and the multi-omics approach, we found the genes related to the key structural domain NB-ARC, which lays the foundation for the study of biologically and abiologically important mechanisms in response to the disease in tea plant.

DOP111 Lack of epithelial RhoA in the gut, a new colitis-associated cancer experimental model

Abstract Background The small GTPase RhoA controls cytoskeleton dynamics in various cell types, including intestinal epithelial cells (IECs). Accordingly, we have shown that lack of RhoA in IECs in mice increases intestinal permeability and inflammation1. However, its role in cancer is controversial. While classically recognized as a potential colorectal cancer (CRC) biomarker2, RhoA inactivation was found to increase Wnt signalling and tumor risk in mouse small intestinal epithelium3. Additionally, proteins in the RhoA/Rac1 pathway were identified as highly mutated in human colitis-associated cancer (CAC)4. We hypothesize that a finely tuned RhoA function in IECs determines CRC risk and that inflammation might modulate RhoA´s pro- or anti-tumor effects in the gut. Methods RhoAΔIEC mice generated using the loxPCre system were our main model1. We monitored disease progression, analysed the transcriptome in colon and tumoral tissue (bulk RNA-sequencing), assessed microbiota composition (16S rRNA gene sequencing), and conducted in vitro colon organoids studies. Moreover, Rho/Rac-associated proteins were analysed across colorectal cancer (CRC) and colitis associated cancer (CAC) mouse models. Results RhoAΔIEC mice developed chronic intestinal inflammation and spontaneous colon tumorigenesis. Bulk RNA sequencing and Gene Set Enrichment Analysis (GSEA) highlighted four regulated pathways: inflammation, microbiota, proliferation, and epithelial-mesenchymal transition (EMT). Transcriptomic changes showed similarities with the azoxymethane/dextran sulphate sodium (AOM/DSS) and APCmin models. Microbiota analysis showed altered β-diversity, with higher abundance of Mycoplasma and Helicobacter genus. Increased Ki67 expression and non-phospho β-catenin indicated Wnt pathway activation, while YAP was not upregulated. RhoA deficient cells showed signs of EMT, as decreased E cadherin expression. Moreover, tumors in RhoAΔIEC mice depicted increased expression of CXCR2-axis chemokines (Cxcl1, 2, 5) and neutrophil infiltration. Among candidate Rho/Rac related proteins, qPCR showed DOCK2 upregulation in AOM and AOM/DSS while Prex2 increased exclusively in AOM/DSS model; DOCK3 and Radil were not regulated. Conclusion Lack of RhoA in IECs drives sustained intestinal inflammation and spontaneous tumorigenesis through Wnt-dependent proliferation, EMT, neutrophil activation, and dysbiosis. RhoAΔIEC mice represent a novel model of inflammation-associated tumorigenesis in the gut. Translationally, the Rac/Rho-associated PREX2 emerges as a candidate CAC-specific biomarker. We hypothesize that PREX2 increases to compensate for RhoA during inflammation.

Timing of exercise differentially impacts adipose tissue gain in male adolescent rats.

Circadian rhythms of metabolic, hormonal, and behavioral fluctuations and their alterations can impact health. An important gap in knowledge in the field is whether the time of the day of exercise and the age of onset of exercise exert distinct effects at the level of whole-body adipose tissue and body composition. The goal of the present study was to determine how exercise at different times of the day during adolescence impacts the adipose tissue transcriptome and content in a rodent model. Rats were subjected to one of four conditions during their adolescence: early active phase control or exercise (EAC or EAE; ZT13), and late active phase control or exercise (LAC or LAE; ZT23). The effects of exercise timing were assessed at the level of subcutaneous and visceral adipose tissue transcriptome, body composition, hypothalamic expression of orexigenic and anorexigenic genes, blood serum markers and 24-hour core body temperature patterns. We found that late active phase exercise (ZT23) greatly upregulated pathways of lipid synthesis, glycolysis and NADH shuttles in LAE rats, compared to LAC or EAE. Conversely, LAE rats showed notably lower content of adipose tissue. In addition, LAE rats showed signs of impaired FGF21-adiponectin axis compared to other groups. Finally, LAE rats showed higher post-exercise core body temperature compared to other groups. Our results thus indicate that our exercise protocol induced an unusual effect characterized by enhanced lipid synthesis but reduced adipose tissue content in late active phase but not early active phase exercise during adolescence.

Amyotrophic Lateral Sclerosis and Parkinson's Disease: Brain Tissue Transcriptome Analysis Reveals Interactions.

This study utilises amyotrophic lateral sclerosis (ALS) and Parkinson's disease (PD) human brain samples from the GEO database and employs differential expression gene (DEG) analysis to identify genes that are pivotal in both neurodegenerative diseases. Through in depth GO and KEGG enrichment analyses, we elucidated the biological functions and potential pathways associated with these DEGs. Furthermore, by constructing protein‒protein interaction networks, we highlight the significance of shared DEGs in both cellular physiology and disease contexts. Analysis of drug‒gene associations revealed potential therapeutic compounds linked to ALS and PD treatment. Additionally, we explored the interactions between transcription factors, miRNAs, and common DEGs, revealing aspects of gene regulatory networks. This study provides insights into the molecular mechanisms of ALS and PD, offering valuable contributions to ongoing research and potential therapeutic avenues.

Divergent roles of m6A in orchestrating brown and white adipocyte transcriptomes and systemic metabolism

N6-methyladenosine (m6A) is among the most abundant mRNA modifications, yet its cell-type-specific regulatory roles remain unclear. Here we show that m6A methyltransferase-like 14 (METTL14) differentially regulates transcriptome in brown versus white adipose tissue (BAT and WAT), leading to divergent metabolic outcomes. In humans and mice with insulin resistance, METTL14 expression differs significantly from BAT and WAT in the context of its correlation with insulin sensitivity. Mettl14-knockout in BAT promotes prostaglandin secretion, improving systemic insulin sensitivity. Conversely, Mettl14-knockout in WAT triggers adipocyte apoptosis and systemic insulin resistance. m6A-seq and RNA-seq integration revealed upregulated prostaglandin biosynthesis pathways in BAT and apoptotic pathways in WAT with Mettl14 deficiency. Stable METTL14-knockout hBAs/hWAs show METTL14-mediated m6A promotes mRNA decay of PTGES2 and CBR1 in hBAs and TRAIL and TNFR1 in hWAs. These data shed light on the ability of m6A to impact metabolism in a cell-type-specific manner with implications for influencing the pathophysiology of metabolic diseases.

Genomic insights into fibrinogen-related proteins and expression analysis in the Pacific white shrimp, Litopenaeusvannamei.

Fibrinogen-related domain (FReD) containing proteins are an evolutionarily conserved immune gene family characterized by the C-terminal fibrinogen (FBG) and diverse N-terminal domains. To understand the complexity of this family in crustaceans, we performed genome screening and identified 43 full-length FReDs encoding genes in Litopenaeus vannamei. Structural classification analysis revealed these putative FReDs could be divided into six types, including two reported types (LvFReDI and II) and four new types (LvFReDIII-VI). Sequence and phylogenetic analysis showed that FBG domains were highly conserved throughout and phylogeny clusters correlated strongly with gene type. We analyzed the temporal and spatial expression patterns of LvFReD genes based on the transcriptomes of developmental stages, adult tissues or pathogen infected tissues of L. vannamei. Most LvFReDs were expressed from larval in membrane stage, and exhibited tissue-specific expression patterns and immune-responsive transcription after challenge with bacteria or virus. Further time-course expression analysis suggested that LvFReDII genes with additional coiled-coil region were more sensitive to pathogens than LvFReDI genes. Our findings provided comprehensive gene sequence resources and expression profiles of FReD genes in shrimp, which give insights into clarifying the diversity and function of these genes in crustaceans.

Dan-Shen-Yin against ethanol-induced chronic gastric mucosal injury in rats by inhibiting apoptosis via IP3R-controlled calcium release.

The pathogenesis of alcoholic gastric injury has long been a significant topic in the medical field. Dan-Shen-Yin (DSY), a classic traditional Chinese medicine formula, has been shown to alleviate gastric mucosal injury and to treat stomachaches in clinical settings. However, the mechanism by which DSY against alcoholic gastric injury requires further investigation. This study aimed to explore the effect and mechanism of DSY in preventing alcohol-induced gastric mucosal injury. The Rat model of alcohol-induced gastric injury (AIGI) was established by gavage with 56% ethanol for 1 month. The protective effect of DSY against AIGI was confirmed. Serum non-targeted metabolomics and gastric tissue transcriptomics were employed to explore the potential mechanisms of DSY in treating alcoholic gastric injury, followed by further verification via Western blotting (WB), Histopathological and Immunohistochemical etc. Additionally, an ionomycin-induced calcium overload model and an ethanol-induced injury model in gastric epithelial cells (GES-1) were established for in vitro experiments. The active ingredients of DSY were screened using flow cytometry, laser confocal microscopy, and molecular docking techniques. Transcriptome analysis indicated that elevated calcium levels were a key pathological change in the gastric tissue of AIGI rats. DSY was found to inhibit the activation of the phosphatidylinositol signaling pathway and reduce calcium levels in serum and gastric tissue. Inositol trisphosphate receptor (IP3R) was identified as a significant potential target of DSY in AIGI rats, where IP3R was activated. Both in vivo(AIGI rats) and in vitro experiments(GES-1 Cell) demonstrated that DSY effectively inhibited the activation of IP3R-mediated calcium signaling pathway (downregulated IP3R, Grp75, VDAC1) and alleviated apoptosis (downregulated Caspase 9, Caspase 3, Cytc, Bax and upregulated Bcl-XL, Bcl-2) caused by elevated calcium levels. Furthermore, compounds including salvianolic acid A, salvianolic acid B, lithospermic acid, and isoorientin from DSY were successfully identified as possessing anti-apoptotic activity and inhibiting IP3R expression. This study suggested that calcium levels were a key pathological change in AIGI rats. DSY could inhibit the activation of the phosphatidylinositol signaling pathway, reduce calcium levels, and inhibit IP3R to repair mitochondrial apoptosis. Salvianolic acid a, salvianolic acid b, lithospermic acid, and isoorientin were potential active ingredients for the treatment of alcoholic gastric injury.

Induction of MASH in three-dimensional bioprinted human liver tissue.

Metabolic dysfunction-associated steatohepatitis (MASH), formerly known as nonalcoholic steatohepatitis (MASH), is a major risk factor for cirrhosis and hepatocellular carcinoma (HCC) and a leading cause of liver transplantation. MASH is caused by an accumulation of toxic fat molecules in the hepatocyte which leads to inflammation and fibrosis. Inadequate human "MASH in a dish" models have limited our advances in understanding MASH pathogenesis and in drug discovery. This study uses complex multicellular 3D bioprinting, combining hepatocytes with nonparenchymal cells in physiologically relevant cell ratios using biocompatible hydrogels to generate bioinks Bioprinted human liver tissues consisting of the four major cell types, (hepatocytes, liver endothelial cells, Kupffer cells, and hepatic stellate cells) are generated from cells purified from normal human livers, using this complex bioprinting platform. These liver tissues are incubated in a cocktail consisting of fatty acids, lipopolysaccharide (LPS), and fructose to produce a MASH phenotype in comparison to liver tissues incubated in control media. Furthermore, these bioprinted liver tissues are of sufficient size to undergo histological processing and immunohistchemistry comparable to classic clinical pathological analysis. The MASH liver tissues develop hepatocyte steatosis, inflammation, and fibrosis, in response to the MASH induction media. Additionally, the transcriptome of the MASH tissues differed significantly from the healthy tissues and more closely resembled the transcriptome of biopsies of MASH livers from patients Thus, this study has developed a MASH bioprinted liver tissue suitable for studies on pathophysiology and drug discovery.

Evaluating sex-specific responses to western diet across the lifespan: impact on cardiac function and transcriptomic signatures in C57BL/6J mice at 530 and 640/750 days of age

BackgroundLong-term consumption of Western Diet (WD) is a well-established risk factor for the development of cardiovascular disease (CVD); however, there is a paucity of studies on the long-term effects of WD on the pathophysiology of CVD and sex-specific responses.MethodsOur study aimed to investigate the sex-specific pathophysiological changes in left ventricular (LV) function using transthoracic echocardiography (ECHO) and LV tissue transcriptomics in WD-fed C57BL/6 J mice for 125 days, starting at the age of 300 through 425 days.ResultsIn female mice, consumption of the WD diet showed long-term effects on LV structure and possible development of HFpEF-like phenotype with compensatory cardiac structural changes later in life. In male mice, ECHO revealed the development of an HFrEF-like phenotype later in life without detectable structural alterations. The transcriptomic profile revealed a sex-associated dichotomy in LV structure and function. Specifically, at 530-day, WD-fed male mice exhibited differentially expressed genes (DEGs), which were overrepresented in pathways associated with endocrine function, signal transduction, and cardiomyopathies. At 750 days, WD-fed male mice exhibited dysregulation of several genes involved in various lipid, glucagon, and glutathione metabolic pathways. At 530 days, WD-fed female mice exhibited the most distinctive set of DEGs with an abundance of genes related to circadian rhythms. At 640 days, altered DEGs in WD-fed female mice were associated with cardiac energy metabolism and remodeling.ConclusionsOur study demonstrated distinct sex-specific and age-associated differences in cardiac structure, function, and transcriptome signature between WD-fed male and female mice.Graphical

Co-exposure to polyethylene microplastics and house dust mites aggravates airway epithelial barrier dysfunction and airway inflammation via CXCL1 signaling pathway in a mouse model.

Environmental pollutants have been found to contribute to the development and acute exacerbation of asthma. Microplastics (MPs) have received widespread attention as an emerging global pollutant. Airborne MPs can cause various adverse health effects. Due to their hydrophobicity, MPs can act as a carrier for other pollutants, pathogens, and allergens. This carrier effect of MPs may adsorb allergens and thus make the body exposed to MPs and a large number of allergens simultaneously. We hypothesized that co-exposure to inhaled MPs and aeroallergens may promote the development of airway inflammation of asthma by disrupting the airway epithelial barrier. The effects of co-exposure to Polyethylene microplastics (PE-MPs) and allergens on allergic airway inflammation and airway epithelial barrier were examined in a mouse model of asthma. The mice were divided into four groups: (i) Control group, treated only with PBS; (ii) MP group, exposed to PE-MPs and PBS; (iii) HDM group, mice were sensitized and challenged with HDM, and intranasally treated with PBS; (iv) HDM+MP group, mice were sensitized and challenged with HDM, and intranasally treated with PE-MPs. Histology and ELISA assays were used to evaluate the severity of airway inflammation. FITC-dextran permeability assay, immunofluorescence assay, and RT-PCR were used to evaluate the airway epithelial barrier function and the expression of relevant molecules. Transcriptomics analysis with lung tissue sequencing was conducted to identify possible pathways responsible for the effects of PE-MPs. Co-exposure of mice to PE-MPs and HDM induced a higher degree of inflammatory cell infiltration, bronchial goblet cell hyperplasia, collagen deposition, allergen sensitization, and Th2 immune bias than exposure to HDM alone. Co-exposure to PE-MPs and HDM aggravated oxidative stress injury in the lung and the production of cytokine IL-33 in the BALF. In addition, co-exposure of mice to PE-MPs and HDM resulted in a more pronounced decrease in the expression of relevant molecules of the airway epithelial barrier and more significant increase in the permeability of airway epithelia. Lung tissue transcriptomics analysis revealed that PE-MPs exposure was associated with CXCL1 signaling and neutrophil activation. Co-exposure to MPs and HDM may promote airway inflammation and airway epithelial barrier disruption and induce immune responses characterized by CXCL1 signaling and neutrophilic inflammation.

Aging2Cancer: an integrated resource for linking aging to tumor multi-omics data

BackgroundAging and tumorigenesis share intricate regulatory processes, that alter the genome, epigenome, transcriptome and immune landscape of tissues. Discovering the link between aging and cancer in terms of multiomics characteristics remains a challenge for biomedical researchers.MethodsWe collected high-throughput datasets for 57 human tumors and 20 normal tissues, including 23,125 samples with age information. On the basis of these sufficient omics data, we introduced six useful modules including genomic (somatic mutation and copy number variation), gene expression, DNA methylation, hallmarks (aging and cancer), immune landscape (immune infiltration, immune pathways, immune signatures, and antitumor immune activities) and survival analysis. Correlation and differential analyses were performed for the multiomic signatures associated with aging at the gene level.ResultsWe developed Aging2Cancer (http://210.37.77.200:8080/Aging2Cancer/index.jsp), which is a comprehensive database and analysis platform for revealing the associations between aging and cancer. Users can search for and visualize the results of genes of interest to explore the relationships between aging and cancer at the gene level for different omics levels.ConclusionsWe believe that Aging2Cancer is a valuable resource for identifying novel biomarkers and will serve as a bridge for linking aging to cancer.

A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes.

Lymph node (LN) lymphatic endothelial cells (LEC) actively acquire and archive foreign antigens. Here, we address questions of how LECs achieve durable antigen archiving and whether LECs with high levels of antigen express unique transcriptional programs. We used single cell sequencing in dissociated LN tissue and spatial transcriptomics to quantify antigen levels in LEC subsets and dendritic cell populations at multiple time points after immunization and determined that ceiling and floor LECs archive antigen for the longest duration. We identify, using spatial transcriptomics, antigen positive LEC-dendritic cell interactions. Using a prime-boost strategy we find increased antigen levels within LECs after a second immunization demonstrating that LEC antigen acquisition and archiving capacity can be improved over multiple exposures. Using machine learning we defined a unique transcriptional program within archiving LECs that predicted LEC archiving capacity in mouse and human independent data sets. We validated this modeling, showing we could predict lower levels of LEC antigen archiving in chikungunya virus-infected mice and demonstrated in vivo the accuracy of our prediction. Collectively, our findings establish unique properties of LECs and a defining transcriptional program for antigen archiving that can predict antigen archiving capacity in different disease states and organisms.

Magnesium Supplementation Modifies Arthritis Synovial and Splenic Transcriptomic Signatures Including Ferroptosis and Cell Senescence Biological Pathways.

Rheumatoid arthritis (RA) is a common systemic autoimmune inflammatory disease that can cause joint damage. We have recently reported that oral magnesium supplementation significantly reduces disease severity and joint damage in models of RA. In the present study, we analyzed the transcriptome of spleens and synovial tissues obtained from mice with KRN serum-induced arthritis (KSIA) consuming either a high Mg supplemented diet (Mg2800; n = 7) or a normal diet (Mg500; n = 7). Tissues were collected at the end of a 15-day KSIA experiment. RNA was extracted and used for sequencing and analyses. There was an enrichment of differentially expressed genes (DEGs) belonging to Reactome and Gene Ontology (GO) pathways implicated in RA pathogenesis such as RHO GTPases, the RUNX1 pathway, oxidative stress-induced senescence, and the senescence-associated secretory phenotype. Actc1 and Nr4a3 were among the genes with the highest expression, while Krt79 and Ffar2 were among the genes with the lowest expression in synovial tissues of the Mg2800 group compared with the Mg500 group. Spleens had an enrichment for the metabolism of folate and pterines and the HSP90 chaperone cycle for the steroid hormone receptor. We describe the tissue transcriptomic consequences of arthritis-protecting Mg supplementation in KSIA mice. These results show that oral Mg supplementation may interfere with the response to oxidative stress and senescence and other processes known to participate in RA pathogenesis. We provide new evidence supporting the disease-suppressing effect of increased Mg intake in arthritis and its potential to become a new addition to the therapeutic options for RA and other autoimmune and inflammatory diseases.

Transcriptomic analysis of pancreatic tissue from humans and mice identifies potential gene signatures and unexplored pathways during progression from acute to chronic pancreatitis.

A comprehensive understanding of the molecular pathogenesis of chronic pancreatitis (CP), a fibroinflammatory disorder of the pancreas, is warranted for the development of targeted therapies. The current study focused on comparing the transcriptomes of pancreatic tissues obtained from patients with CP with those of two rodent models of chemically induced CP to identify dysregulated genes/signaling pathways. Pancreatitis was induced in mice using cerulein and L-arginine. Pncreatic tissues were obtained from humans and mice. The RNA was isolated, and the transcriptomes were generated using the GeneChip Human Transcriptome Array 2.0 and Clariom D Mouse Array respectively. Differentially expressed genes with log2-fold changes ≥ +2 and ≤ -2 were considered for functional and signaling pathway enrichment analysis. The expression of NUCB2, which plays a role in β-cell function, was validated by ELISA in acute pancreatitis (AP) and immune cell responses in AP and CP using flow cytometry. The current study identifies L-arginine-induced CP as a better model for investigating the pathogenesis of human CP, with greater similarity in dysregulated genes (22%), transcription factors (34%) and enriched pathways (58%) compared to cerulein model (2%, 11% and 9%) respectively. Nesfatin-1, encoded by NUCB2, was decreased in patients with AP (12% nondiabetic, 41% post pancreatitis diabetes). The Th1 immune cell response was greater in the patients with AP (44%), whereas Th17 immune response was greater in patients with CP (18%). Our study highlights potential novel and unexplored pathways involved in inflammation, fibrosis, and pain in CP and paves the way for testing them as putative drug targets using a severe disease model.

DeepCORE: An interpretable multi-view deep neural network model to detect co-operative regulatory elements

Gene transcription is an essential process involved in all aspects of cellular functions with significant impact on biological traits and diseases. This process is tightly regulated by multiple elements that co-operate to jointly modulate the transcription levels of target genes. To decipher the complicated regulatory network, we present a novel multi-view attention-based deep neural network that models the relationship between genetic, epigenetic, and transcriptional patterns and identifies co-operative regulatory elements (COREs). We applied this new method, named DeepCORE, to predict transcriptomes in various tissues and cell lines, which outperformed the state-of-the-art algorithms. Furthermore, DeepCORE contains an interpreter that extracts the attention values embedded in the deep neural network, maps the attended regions to putative regulatory elements, and infers COREs based on correlated attentions. The identified COREs are significantly enriched with known promoters and enhancers. Novel regulatory elements discovered by DeepCORE showed epigenetic signatures consistent with the status of histone modification marks.

A prognostic molecular signature of hepatic steatosis is spatially heterogeneous and dynamic in human liver.

Hepatic steatosis is a central phenotype in multi-system metabolic dysfunction and is increasing in parallelwith the obesity pandemic. We use a translational approach integrating clinical phenotyping and outcomes, circulating proteomics, and tissue transcriptomics to identify dynamic, functional biomarkers of hepatic steatosis. Using multi-modality imaging and broad proteomic profiling, we identify proteins implicated in the progression of hepatic steatosis that are largely encoded by genes enriched at the transcriptional level in the human liver. These transcripts are differentially expressed across areas of steatosis in spatial transcriptomics, and several are dynamic during stages of steatosis. Circulating multi-protein signatures of steatosis strongly associate with fatty liver disease and multi-system metabolic outcomes. Using a humanized "liver-on-a-chip" model, we induce hepatic steatosis, confirming cell-specific expression of prioritized targets. These results underscore the utility of this approach to identify a prognostic, functional, dynamic "liquid biopsy" of human liver, relevant to biomarker discovery and mechanistic research applications.

Lipopolysaccharide in Bile Promotes the Neutrophil Extracellular Traps-Induced Gallstone Formation by Activating the Gallbladder Immune Barrier.

Cholelithiasis areis a common digestive system disorder, with cholesterol gallstones being the most prevalent type. Gallstones lead to many severe complications, posing a significant burden on global healthcare systems. Many studies have shown associations between biliary microbiota, gallbladder immune microenvironment, and gallstone formation. However, the specific immune mechanisms underlying the cholesterol gallstone formation have not been fully elucidated. In this study, gallbladderand bile samples from 8 asymptomatic patients with cholelithiasis undergoing cholecystectomy and 11healthy liver transplant donors were collected for tissue transcriptome sequencing and differential analysis. Male C57BL/6J mice were fed a normal or lithogenic diet for 6weeks. Starting from the third week, lipopolysaccharide (LPS) or specific regulators were injected intraperitoneally once a week for a total of 3 times. Enzyme-linked immunosorbent assay, quantitative polymerase chain reaction, Western blot, immunohistochemistry, and immunofluorescence were employed for quantitative, qualitative or localization analysis of LPS, neutrophil extracellular traps (NETs), inflammatory factors, proteins, and mRNAs using samples collected from mice. In patients with cholelithiasis, the gallbladder mechanical barrier is impaired, resulting in an immune-activated state. LPS induces damage to the gallbladder mucosal mechanical barrier through the Toll-like receptor 4 (TLR4)/myeloid differentiation factor 88 (MyD88)/nuclear factor kappa-B (NF-κB) signaling pathway. Furthermore, it stimulates the continuous production of NETs through the TLR4/Phosphoinositide 3-kinase (PI3K)/Protein kinase B (Akt) signaling pathway, aggravating the formation of gallstones. With the biliary dysbiosis, excessive LPS can invade the submucosa of the gallbladder, leading to chronic inflammation that recruits neutrophils to form NETs, which are ultimately expelled into bile, thereby promoting the formation of gallstones.